Just a couple thoughts.
I would start with a debugging stacktrace:
use Carp;
$SIG{ALRM} = sub { Carp::cluck("HERE") };
alarm 10;
# ... now proceed with files
This would print a stacktrace after 10 seconds of execution, providing pointers about where the code is.
Alternatively you can bind to $SIG{INT} and press Ctrl-C to see where you are.
Or you can use $logger->info(Carp::longmess("HERE")); instead or cluck.
Also I'm wondering whether the script has a use strict; in it. Because if it doesn't, debugging becomes twice as hard.
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